Dermoscopy is a skin surface microscopic technique allowing specular reflection free observation of the skin, and has been used to examine pigmented skin lesions. However, dermoscopy has limitations in providing depth information due to lack of 3D resolution. In order to overcome the limitations, we developed dermoscopy guided multi-functional optical coherence tomography (MF-OCT) providing both high-contrast superficial information and depth-resolved structural, birefringent, and vascular information of the skin simultaneously. Dermoscopy and MF-OCT were combined by using a dichroic mirror, and dark-field configuration was adapted for MF-OCT to reduce specular reflection. After characterization, dermoscopy guided MF-OCT was applied to several human skin lesions such as the scar, port-wine stain (PWS) as well as the normal skin for demonstration. Various features of the scar and PWS were elucidated by both dermoscopy and MF-OCT. Dermoscopy guided MF-OCT may be useful for evaluation and treatment monitoring of skin lesions in clinical applications.